Unusual Residues

This tab gives considerably more control over the view of residue distributions also seen in the Numbering & Regions tab. Distributions of amino acids are obtained from numbered positions in the abYsis database.

By default, the tab is used to identify unusual residues in the sequence of interest, although it can also be used to look at all residues. (The Humanize tab is a more effective way of looking at all residues.)

By default, an unusual residue is defined as one that occurs at the given position in ≤10% of sequences which have that position.

Controls

The Comparison Organism dropdown is used to restrict the calculation of distributions to a particular organism. Only the top 15 organisms are included where counts are sufficient to obtain some meaningful data.

The Numbering Scheme dropdown is used to change the numbering scheme: Chothia, Kabat or Chothia+/Martin schemes may be selected. See the About / Definitions page for a description of the different schemes.

The Threshold dropdown is used to change the threshold considered to be unusual. If this is set to None, then no threshold will be used and all residues in the sequence will be displayed.

Results

The Results table shows positions where the freqeuency of the query residue is less than the specified threshold.>/p>

The first row of the table shows the residues from the sequence of interest.

The second row of the table shows the residue number according to the chosen numbering scheme.

If you click on a residue number, the Distribution panel will be updated. (See below.)

The third row shows the frequency of the residue from the sequence if information at each position in the selected comparison organisms.

The fourth row shows the most common residues at each position (frequency > 10%).

Below the table is shown the framework and CDR regions according to different regions definitions. See the About / Distributions page for information.

Below the region indicators, particularly unusual residues (frequency less than 1%) are highlighted using a vertical arrow.

Distributions

A bar chart of the residue distribution for the selected residue is displayed. The residue present in the sequence of interest is highlighted with a downwards arrow at the top of the bar. Below is an associated table containing the residue counts in non-identical sequences and the relative frequencies. You may also download a version of the graph and a CSV file of the data.

Click the residue numbers in the main table to change the distribution that is displayed in the graph.

Tools

If there are atom coordinates available for the query sequence, the Display in Structure button will appear. Click this to change automatically to the Structure tab with all the residues shown in the current table pre-highligted in the structure viewer.